CF is a genetic disease associated with debilitating and terminal lung infections. The bacterial lung pathogen Pseudomonas aeruginosa chronically colonizes the lungs of more than 80% of patients with CF, and its presence is strongly associated with worse patient status. However, it is clear that factors other than the presence of P. aeruginosa impact the rate and extent of lung damage in P. aeruginosa-infected patients. More than a dozen studies have found that fungi also inhabit the lungs of the majority of individuals with CF, published clinical data report correlations between the presence of fungi in culture and worse lung function or increased frequency of disease exacerbations. In two studies, researchers found that patients colonized with both P. aeruginosa and fungi, such as Candida albicans or Aspergillus fumigatus, were worse off than those not co-colonized by fungi. Based on published and preliminary data, we hypothesize that the dynamics between airway bacteria and fungi strongly impact CF lung disease in two ways. First, we hypothesize that the suppression of bacteria during periods of antibacterial therapy leads to high fungal loads that can be harmful to airways (tested in Aim 1). As part of these studies, we will develop methods for the analysis of fungal communities in collaboration with Dr. Mitchell Sogin (MBL) and Dr. Jason Stajich, (UC Riverside) using longitudinally collected clinical samples from patients undergoing systemic antibiotic therapy. In addition to analysis of the changes in fungi species, we will determine if specific fungi increase in absolute levels, how the bacterial communities change in conjunction with changes in the fungal communities, and how fungi impact the host over the course of treatment. Second, we hypothesize that molecular interactions between P. aeruginosa and fungi such as C. albicans and other Candida spp. increase P. aeruginosa virulence in mixed bacterial and fungal infections (tested in Aim 2). We will use a combination of cell culture models and clinical studies, in combination with cutting edge RNA analysis methods, in an iterative process to understand the dynamics of bacteria and fungi in the CF lung. Our long term goals are: (i) to determine if CF patients colonized with fungi would benefit from existing antifungal therapies that are currently only routinely administered to a small subset of CF patients, and (ii) to develop strategies for the analysis of other chronic, polymicrobial infections involving fungi and bacteria, and the interactions that occur between microbes within polymicrobial communities.